Cracked roof

if it is where aluminum and fiberglass come together under the caulk, then the best you can do is scrape the caulk off as good as you can, clean the two surfaces up with mineral spirits or something to get them clean, then re-apply new sealant.  it doesn't sound like you are talking about holes or cracks in the roof, but rather at a seem, a good picture or two would help a lot to see what you are talking about.  

there is also proper sealants and not proper sealants to use, make sure you use proper ones, and you could even look into better sealants, but they are way more expensive.  as long as your willing to climb up every year and look at the joints and touch up areas than need it, the normal self leveling rv sealant will work just fine on the roof, and non sag on the sides.  one thing though if sealing up around plastic vents and such, find a plastic primer that will improve the bond from sealants to plastic.  to many times I find it just isn't sticking around skylights very good.  THIS is a good one, but there are others, this is just an example of what I am talking about.  

I am not a fan of eternabond tape for anything but emergency repairs myself, it is expensive, and if not installed correctly prone to fail.  I am still waiting for long term results from sun exposure and stuff, I want to see how it holds up after 5 or 10 years.